Best RNA-seq program for unpaired reads

Aman Mahajan

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Join Date: Jan 2012

Posts: 22
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#16

02-02-2012, 01:18 AM

Installation of RSEQ - help required.

Originally posted by jgibbons1 View Post

I really like the program rSeq by Hui Jiang.

1st convert your reads to standard fasta format. The software has a mapping program and then a script that calculates RPKM for each reference transcript.

Also...its free!

I am having problem running RSEQtools. This is the installation procedure.

Installation
============

The installation steps have to be executed in the following order:

1) Install the GNU Scientific Library

( I have done the 1st step)

2) Install BIOS - Have not been able to carry out this step.

- Set the following environment variables:
BIOINFOCONFDIR=/pathTo/RSEQtools/bios/conf
BIOINFOGSLDIR=/pathTo/gsl-X.XX

- Compiling BIOS:
cd pathTo/RSEQtools/bios
make
make prod

Thanks .
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